My male rabbit has got in to my female rabbits run and mated with her?

Well... depending on your rabbit's age, if they are younger rabbits (Anywhere from six months to a year and a half) it is likely that they are both pregoes. (Pregnant) The sister should be fine with the other rabbit, I had two sisters in the same pen when my baby bunnies were born(It was the same cirstance as yours, I didn't even see them mate). The only thing that is likely to happen will be that the one sister with chew the hair off of the other to line her nest with. If they are show rabbits, I would take her out, because even though it does not hurt the other rabbit to have her hair pulled out, it can b unsightly. But.... I doubt it will matter because both bunnies have probably had access to a buck. Have fun with you baby bunnies!!